Tom Burghardt wrote: > I would like to make a DOPE profile for a modeled protein containing a > chemically modified side chain. I used the script suggested in the > Advanced Tutorial with the following lines to read the library files > containing information about the modified residue. > > env = environ(restyp_lib_file='${LIB}/restyp_tom.lib') > env.libs.topology.read(file='$(LIB)/top_heav_tom.lib') # read topology > env.libs.parameters.read(file='$(LIB)/par_tom.lib') # read parameters > > The DOPE profile is created by the script but the modified residue is left > out of the profile. > > Any suggestions would be appreciated.

DOPE is a statistical potential, derived from the known distributions of standard residue types in PDB. Thus, by definition, it cannot tell you anything about non-standard residues; you would have to rederive the potential including examples of your modified residue, which is not a trivial task.

A 'regular' profile should work just fine, since the default (non-DOPE) potential acts on known _atom_ types.

Ben Webb, Modeller Caretaker